Hi Max, Could you send a snapshot of an area where your wm edits did not have an effect? Keep in mind the wm voxels you add to the wm.mgz should be well connected to the rest of the wm mask, or else it will tend to get pruned off. You can look at the ?h.orig.nofix surfaces to see if the intial surface model includes your wm edits. -Louis
On Mon, 23 Jun 2014, Max Svensson wrote:
Hi! When I edit my data, for instance wm editing, I do not see the changes applied to the original image. To make you understand what I do: Open up freeview, load the image, Wm and brainmask, with wm at the top. Then I go into voxel edit, press recon edit, and start filling in topographical defects and do some wm editing. HOWEVER, after I run recon all (recon-all -autorecon2 -autorecon3 -subjid anon)and it's finished without problems, I do not see the edits done on my image. Sure, I see the yellow colour which I filled some spots with, but I was thinking that I would see an edited image, that is with pia (topographical defects) and wm surface going out to the areas I edited. Not only yellow filling which was there before since I edited. Am I doing something wrong? Is the reconprocessed images hidden out there somewhere? Freesurfer team, please help!
Best, MAX